Question: Pool male and female individuals for de novo transcriptome assembly?
0
gravatar for nsimons
2.8 years ago by
nsimons0
nsimons0 wrote:

Hi, I have what I think is a simple question:

Is it appropriate to combine reads from males and females for de novo transcriptome assembly?

I have an RNAseq dataset consisting of 8 females and 21 males, I've done a de novo assembly on a single individual as a first pass and it looks pretty good, but it makes sense to leverage the amount of data I have for a more complete transcriptome. Is there any potential issue with combining both sexes?

Thanks!

rna-seq assembly • 742 views
ADD COMMENTlink modified 2.8 years ago by WouterDeCoster42k • written 2.8 years ago by nsimons0
0
gravatar for WouterDeCoster
2.8 years ago by
Belgium
WouterDeCoster42k wrote:

Well, apart from sex chromosomes and gender-specific expression on those, I don't think there is a reason not to combine all your data.

As a sanity check, you could also assemble all males and compare that to the assembly of all animals.

ADD COMMENTlink written 2.8 years ago by WouterDeCoster42k
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